https://www.ens-lyon.fr/LBMC https://www.ens-lyon.fr/LBMC/equipes/complexite-plasticite-et-roles-des-miarns/publications/JouravlevaZamore2025 Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals. 2025-01-28T05:13:19Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/dynamics-and-control-of-biological-assemblies-and-macromolecular-machines/publications/GobetEtAl2025 Multidrug ABC transporters harness the energy of ATP binding and hydrolysis totranslocate substrates out of the cell and detoxify them. While this involves awell-accepted alternating access mechanism, molecular details of this interplayare still elusive. Rhodamine6G binding on a catalytic inactive mutant of thehomodimeric multidrug ABC transporter BmrA triggers a cooperative binding of ATPon the two identical nucleotide-binding-sites, otherwise michaelian. Here, weinvestigate this asymmetric behavior via a structural-enzymology approach,solving cryoEM structures of BmrA at defined ATP ratios, highlighting theplasticity of BmrA as it undergoes the transition from inward to outward facingconformations. Analysis of continuous heterogeneity within cryoEM data andstructural dynamics, reveals that Rhodamine6G narrows the conformational spectrumexplored by the nucleotide-binding domains. We observe the same behavior for theother drug Hœchst33342. Following on these findings, the effect of drug-bindingshowed an ATPase stimulation and a maximal transport activity of the wild-typeprotein at the concentration-range where the cooperative transition occurs.Altogether, these findings provide a description of the influence of drug bindingon the ATP-binding sites through a change in conformational dynamics. 2025-03-05T10:21:16Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/NematodeCell/publications/Letcher2025 2025-07-08T19:43:25Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/epigenetique-et-formation-du-zygote/publications/KeaisEtAl2025 Meiotic drivers are selfish genetic elements that bias their own transmission during meiosis or gamete formation. Due to the fundamental differences between male and female meiosis in animals and plants, meiotic drivers operate through distinct mechanisms in the two sexes: In females, they exploit the asymmetry of meiosis to ensure their inclusion in the egg, whereas in males, they eliminate competing gametes after symmetric meiosis. Meiotic drive is commonly reported in males, where it strongly influences the evolution of spermatogenesis, while the few known cases in females have highlighted its crucial role in centromere evolution. Despite a growing number of examples in a wide range of organisms, meiotic drive has so far only been observed in one sex or the other since its discovery nearly 100 y ago. Here, we show that a selfish X chromosome known to cause meiotic drive in male Drosophila testacea flies also causes meiotic drive in females. We find that this X chromosome has supergene architecture, harboring extensive structural rearrangements that suppress recombination between the two X chromosomes. This has contributed to a substantial expansion of its size compared to the wild-type chromosome, partly due to the accumulation of species-specific repetitive elements. Our findings suggest that female meiotic drive may play an important role in the evolutionary dynamics of polymorphic structural variants that suppress recombination, including inversions, translocations, and supergenes. 2025-04-25T18:11:19Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/controle-de-l2019expression-genetique-et-oncogenese-virale/publications/HuangEtAl2025 NARROW LEAF 1 (NAL1), originally identified for its role in shaping leafmorphology, plant architecture, and various agronomic traits in rice, hasremained enigmatic in terms of the molecular mechanisms governing itsmultifaceted functions. In this study, we present a comprehensive structuralanalysis of NAL1 proteins, shedding light on how NAL1 regulates the phaseseparation of its physiological substrate, FRIZZY PANICLE (FZP), a transcriptionfactor. We determined that NAL1 assembles as a hexamer and forms a molecular cagewith a wide central channel and three narrower lateral channels, which coulddiscriminate its different substrates into the catalytic sites. Most notably, ourinvestigation unveils that FZP readily forms molecular condensates via phaseseparation both in vitro and in vivo. NAL1 fine-tunes FZP condensation,maintaining optimal concentrations to enhance transcriptional activity. Whilephase separation roles include sequestration and suppression of transcriptionalor enzymatic activity, our study highlights its context-dependent contribution totranscriptional regulation. NAL1 assumes a pivotal role in regulating the statesof these molecular condensates through its proteolytic activity, subsequentlyenhancing transcriptional cascades. Our findings offer insights intocomprehending the molecular mechanisms underpinning NAL1's diverse functions,with far-reaching implications for the field of plant biology. Additionally,these insights provide valuable guidance for the development of rational breedingstrategies aimed at enhancing crop productivity. 2025-05-15T14:20:02Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/controle-de-l2019expression-genetique-et-oncogenese-virale/publications/RobinMocquet2025 Helicases are enzymes involved in all aspects of nucleic acid synthesis,regulation and degradation. As a consequence, several methods were developed tomonitor their enzymatic activity. In this report, we described an improvement ofbulk fluorescent helicase assays to overcome their specific limitations (cost,health and safety regulations, etc.). Using a real time detection thermocycler tomonitor the fluorescence in real-time, we managed to precisely control theinitiation of the helicase reaction through temperature tuning. Therefore, wewere able to demonstrate that this setup could provide a qualitative and aquantitative evaluation of the helicase domain of the UPF1 helicase (UPF1-HD) andthat several fluorophores could be used in parallel during the same run. 2025-05-15T14:20:02Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/controle-de-l2019expression-genetique-et-oncogenese-virale/publications/NuccetelliEtAl2025 The nonsense-mediated mRNA decay (NMD) pathway triggers the degradation ofdefective mRNAs and governs the expression of mRNAs with specificcharacteristics. Current understanding indicates that NMD is often significantlysuppressed during viral infections to protect the viral genome. In numerousviruses, this inhibition is achieved through direct or indirect interference withthe RNA helicase UPF1, thereby promoting viral replication and enhancingpathogenesis. In this study, we employed biochemical, biophysical assays andcellular investigations to explore the interplay between UPF1 and thenucleocapsid (Np) protein of SARS-CoV-2. We evaluated their direct interactionand its impact on inhibiting cellular NMD. Furthermore, we characterized how thisinteraction affects UPF1's enzymatic function. Our findings demonstrate that Npinhibits the unwinding activity of UPF1 by physically obstructing its access tostructured nucleic acid substrates. Additionally, we showed that Np bindsdirectly to UPF2, disrupting the formation of the UPF1/UPF2 complex essential forNMD progression. Intriguingly, our research also uncovered a surprising pro-viralrole of UPF1 and an antiviral function of UPF2. These results unveil a novel,multi-faceted mechanism by which SARS-CoV-2 evades the host's defenses andmanipulates cellular components. This underscores the potential therapeuticstrategy of targeting Np-UPF1/UPF2 interactions to treat COVID-19. 2025-05-15T14:20:02Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/NematodeCell/publications/BlancEtAl2025 Asexuality is a derived character, and asexual species have emerged multipletimes independently throughout evolution. In animals, parthenogenesis, whereby azygote inherits only its mother genome, requires female meiosis modification toproduce unreduced gametes and compensate for the lack of outcrossing. Variouschanges in the meiotic steps have been identified. Here, we propose a simplifiednomenclature when discussing asexuality in animals, as the existing terminologyhas caused many misinterpretations and may impede interdisciplinarycollaboration. We also shed light on the constraints related to these meioticmodifications in asexual animals and their consequences on their genome. Whenrecombination is preserved in parthenogens, most meiotic modifications should,according to Mendel's second law, result in a loss of heterozygosity (LOH). Onthe other hand, LOH can be prevented if recombination is either abolished orstrongly reduced during meiotic prophase. Surprisingly, several recent exampleshave demonstrated that LOH can be prevented despite recombination. We willdescribe these examples in detail as they illustrate the constraints underlyingthe origin and evolution of asexuality. We also emphasize that the majority ofmechanisms remain unknown in many species. This highlights the need to revisitthe old literature using state-of-the-art cytological imaging and genomictechniques to shed light on these unexplored processes. 2025-07-07T15:09:23Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/epigenetique-et-formation-du-zygote/publications/DubruilleEtAl2025 2025-07-09T05:20:11Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/mecanique-du-genome/publications/Djeghmoum.2025-08-27.8332427169 DNA is a substrate for competing protein-mediated activities. Whether and how transcription and the synaptic steps of recombination collide or are coordinated has not been investigated. Here, using a controlled break induction system and physical detection of D-loop DNA joint molecules in S. cerevisiae, we show that donor transcription by RNA polymerase II strongly and acutely suppresses D-loops in cis. The extent of this suppression depends on the orientation of transcription, suggesting the preferential usage of one end for the repair of DNA break in transcribed regions. Transcription-mediated D-loop suppression does not rely on endogenous transcription factors, the RNA product, or RNA:DNA hybrids. It is independent of, and can be more potent than the conserved trans D-loop-disruption factors Sgs1-Top3-Rmi1BLM-TOPO3α-RMI1/2, Mph1FANCM, and Srs2. This transcription-mediated control promotes genome maintenance by inhibiting ectopic recombination and multi-invasion-induced rearrangements, while authorizing allelic inter-homolog repair. These findings reveal the prioritization between two universal DNA-dependent processes and its role in promoting genome stability. 2025-10-03T07:12:02Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/mecanique-du-genome/publications/meneu.2025 In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of coevolution. Using bacterial genomes integrated into Saccharomyces cerevisiae , which diverged from yeast more than 2 billion years ago, we show that nucleosomes, cohesins, and associated transcriptional machinery can lead to the formation of two different chromatin archetypes, one transcribed and the other silent, independently of heterochromatin formation. These two archetypes also form on eukaryotic exogenous sequences, depend on sequence composition, and can be predicted using neural networks trained on the native genome. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalization, reminiscent of the organization of vertebrate nuclei. 2025-08-27T12:24:41Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/controle-de-l2019expression-genetique-et-oncogenese-virale/publications/SongEtAl2025 RECQ1, the most abundant RecQ helicase in human cells, is involved in telomeremaintenance in ALT cells and plays a critical role in maintaining genomicintegrity and stability. Here, we present five high-resolution crystal structuresthat systematically reveal a novel mechanism by which the RECQ1 helicaserecognizes and regulates G-quadruplex (G4) DNA structures. Our resultsdemonstrate that DNA binding induces intra-subunit rearrangement in RECQ1,transitioning it from a closed to an open conformation. This rearrangement altersthe stability of the dimer interface. G4 recognition and unwinding are driven bycoordinated interactions between the D1/D2 domains and the single-stranded DNA(ssDNA)-binding channel. This dual engagement aligns the G4 tetrad in a geometryfavorable for unwinding. ATP hydrolysis facilitates ssDNA translocation,positioning the β-hairpin to disrupt hydrogen bonds-unraveling G4 structures in amanner analogous to the unwinding of dsDNA. This study proposes a mechanisticmodel for RECQ1-mediated G4 unwinding and elucidates how RECQ1 recognizes andunwinds distinct DNA structures. 2025-10-14T21:52:59Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/controle-de-l2019expression-genetique-et-oncogenese-virale/publications/ProchassonEtAl2025 The hijacking of CRM1 export is an important step of the retroviral replicationcycle. Here, we investigated the consequences of this hijacking for the host.During HTLV-1 infection, we identified that this hijacking by the viral proteinRex favours the association between CRM1 and the RNA helicase UPF1, leading to adecreased affinity of UPF1 for cellular RNA and its nuclear retention. As aconsequence, we found that the nonsense-mediated mRNA decay (NMD), known to havean antiviral function, was inhibited. Corroborating these results, we described asimilar process with Rev, the functional homolog of Rex from HIV-1. Unexpectedly,we also found that, for HTLV-1, this process is coupled with the specific loadingof UPF1 onto vRNA, independently of NMD. In this latter context, UPF1 positivelyregulates several steps of the viral replication cycle, from the nuclear exportof vRNA to the production of mature viral particles. 2025-10-14T21:52:59Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine/publications/TheulotEtAl2025 Current temporal studies of DNA replication are either low-resolution or requirecomplex cell synchronisation and/or sorting procedures. Here we introduceNanotiming, a single-molecule, nanopore sequencing-based method producinghigh-resolution, telomere-to-telomere replication timing (RT) profiles ofeukaryotic genomes by interrogating changes in intracellular dTTP concentrationduring S phase through competition with its analogue bromodeoxyuridinetriphosphate (BrdUTP) for incorporation into replicating DNA. This solely demandsthe labelling of asynchronously growing cells with an innocuous dose of BrdUduring one doubling time followed by BrdU quantification along nanopore reads. Wedemonstrate in S. cerevisiae model eukaryote that Nanotiming reproduces RTprofiles generated by reference methods both in wild-type and mutant cellsinactivated for known RT determinants. Nanotiming is simple, accurate,inexpensive, amenable to large-scale analyses, and has the unique ability toaccess RT of individual telomeres, revealing that Rif1 iconic telomere regulatorselectively delays replication of telomeres associated with specific subtelomericelements. 2025-10-16T14:21:01Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine/publications/BontonouEtAl2025 MOTIVATION: Many machine learning (ML) models developed to classify phenotypefrom gene expression data provide interpretations for their decisions, with theaim of understanding biological processes. For many models, including neuralnetworks, interpretations are lists of genes ranked by their importance for thepredictions, with top-ranked genes likely linked to the phenotype. In thisarticle, we discuss the limitations of such approaches using integrated gradient,an explainability method developed for neural networks, as an example. RESULTS:Experiments are performed on RNA sequencing data from public cancer databases. Acollection of ML models, including multilayer perceptrons and graph neuralnetworks, are trained to classify samples by cancer type. Gene rankings fromintegrated gradients are compared to genes highlighted by statistical featureselection methods such as DESeq2 and other learning methods measuring globalfeature contribution. Experiments show that a small set of top-ranked genes issufficient to achieve good classification. However, similar performance ispossible with lower-ranked genes, although larger sets are required. Moreover,significant differences in top-ranked genes, especially between statistical andlearning methods, prevent a comprehensive biological understanding. Inconclusion, while these methods identify pathology-specific biomarkers, thecompleteness of gene sets selected by explainability techniques for understandingbiological processes remains uncertain. AVAILABILITY AND IMPLEMENTATION: Pythoncode and datasets are available at https://github.com/mbonto/XAI_in_genomics. 2025-10-16T14:21:01Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine/publications/LageEtAl2025 2025-10-16T14:21:59Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/gisv-new/publications/Martin2025.11.22.689898 Gene expression regulation is a stochastic process that can be modified by mutations not only in a deterministic manner but also in a probabilistic way, for example by changing the extent of cell-to-cell variability in gene expression (also called “gene expression noise”) without necessarily changing the expected (mean) expression level. Such mutations can act either in cis (perturbing expression noise at their own locus) or in trans (perturbing expression noise of a gene located elsewhere in the genome). Although systematic studies have successfully analyzed the properties of cis-acting mutations modulating gene expression noise, less is known about the type of genetic changes that may alter expression noise in trans. Here, we applied genetic mapping on yeast strains (Saccharomyces cerevisiae) generated by random mutagenesis and identified three mutations (in chs1, yme2 and msh1 genes) that changed the expression noise of a reporter gene in the nuclear genome regulated by the yeast TDH3 promoter. Each of these mutations affected either extrinsic noise (variability due to cell-specific factors), intrinsic noise (inherent variability within each cell), or both. Surprisingly, all three mutations targeted proteins located outside of the nucleus: Yme2 and Msh1 being involved in the maintenance of mitochondrial genome integrity, and Chs1 being necessary for the repair of cell-wall defects in freshly-born daughter cells. Our results reveal that mitochondrial state can modulate the extent of intrinsic expression noise of eukaryotic nuclear genes.Competing Interest StatementThe authors have declared no competing interest.Illumina sequencing data have been deposited on the European Nucleotide Archive of the EBI under Study PRJEB104107 (https://www.ebi.ac.uk/ena/browser/home). This includes data for genome sequencing of the five EMS mutant strains described in the study, as well as data for deep genome sequencing of three bulks of segregants sorted based on fluorescence (BSA-seq data) for each of the five mutants crossed to the mapping strain YPW1240.Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0022École Normale Supérieure de Lyon, R02/B-R02-FR-S60European Research Council, 101126053_ERC-2023-COGNational Institutes of Health, R01GM108826, R35GM118073U.S. National Science Foundation, https://ror.org/021nxhr62, MCB-1929737European Molecular Biology Organization, LTF-1114-2012 2026-05-27T16:51:08Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/ApoDroso/publications/CelleEtAl2025 Beta-propeller protein-associated neurodegeneration (BPAN) is a rare neurologicaldisorder characterized by severe cognitive and motor impairments. BPAN is causedby de novo pathogenic variants in the WDR45 gene on the X chromosome. WDR45 geneencodes the protein WDR45/WIPI4, a known regulator of autophagy. A defectiveautophagy has been observed in cellular models of BPAN disease and is associatedwith neurological dysfunctions in wdr45 knockout (KO) mice. However, it remainsunclear whether the autophagic defect directly contributes to all WDR45loss-induced phenotypes or whether other WDR45-dependent cellular functions areinvolved. To investigate this, we generated a CRISPR/Cas9-mediated KO of CG11975(dwdr45 KO), the Drosophila homolog of WDR45. Our analysis revealed that dwdr45KO flies display BPAN-like phenotypes, including impaired locomotor function,seizure-like behavior, autophagy dysregulation and iron dyshomeostasis.Additionally, dwdr45 KO flies exhibit shortened lifespan compared to controlflies. These findings demonstrate that dwdr45 KO fly is a relevant in-vivo modelfor investigating the key cellular and molecular mechanisms underlyingBPAN-associated phenotypes. Here we showed that induction of autophagy in dwdr45KO flies improved both the shortened lifespan and the seizure-like behavior, butdid not restore locomotor function. This suggests that defective autophagycontributes to some, but not all, aspects of the phenotypes resulting from lossof dWdr45 function. 2026-01-16T10:13:41Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine/publications/DasaroEtAl2025 2026-10-14T14:47:06Z ArticleReference https://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine/publications/LuthiEtAl2025 Transcriptional enhancers must locate target genes with precision. In mammals,topologically associating domains (TADs) guide this process, but the C. elegansgenome lacks such organization despite containing over 30,000 putative enhancers.Using high-resolution Hi-C, we identify distinct 3D chromatin structures aroundactive enhancers, termed fountains. These ~38 kb cohesin-dependent structures areunique to active enhancers and enriched for topoisomerases and negativelysupercoiled DNA, indicating topological stress. Disrupting cohesin collapsesfountains and leads to transcriptional upregulation of nearby genes, suggestingfountains act as spatial repressors controlling enhancer-promoter communication.This repression preferentially affects neuronal genes, including skn-1/Nrf, whichchanges isoform usage upon cohesin loss in ASI neurons. Cohesin cleavage alsoalters nematode movement and foraging behavior, linking 3D genome architecture toneural function and behavior. Thus, fountains represent a distinctive chromatinfeature that may ensure enhancer specificity in a TAD-less genome. 2026-10-14T14:31:11Z ArticleReference